From 0a7895a17bc2140c2e59ec04a8206102731ba5fd Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 24 Aug 2007 15:37:12 +0000
Subject: [PATCH] remove null pointer exception when embl file is not
retrieved and comment about selecting for peptide or na
sequences
---
src/jalview/ws/dbsources/EmblXmlSource.java | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 1300c65..3179110 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -23,10 +23,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
super();
}
/**
- * set this to false to *not* add protein products to alignment dataset.
- */
- public boolean getProteinProducts=false;
- /**
* retrieve and parse an emblxml file
* @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml
* @param query
@@ -53,13 +49,19 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
}
if (reply != null && reply.exists())
{
+ efile=null;
file = reply.getAbsolutePath();
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ if (reply.length()>25)
+ {
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ } else {
+ result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim());
+ }
}
if (efile!=null) {
for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false,!getProteinProducts, emprefx);
+ SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry
if (seqparts!=null) {
SequenceI[] newseqs = null;
int si=0;
--
1.7.10.2